get_kegg_compounds: Gather all Compounds from all pathways for a given species.

In elsayed-lab/hpgltools: A pile of (hopefully) useful R functions

Gather all Compounds from all pathways for a given species.

Description

This function attempts to iterate over every pathway for a given abbreviation/species and extract from them the set of compounds. This was mostly copy/pasted from get_kegg_genes.

Usage

get_kegg_compounds(
  pathway = "all",
  abbreviation = NULL,
  species = "leishmania major",
  savefile = NULL
)

Arguments

pathway	One or more pathways, all does what it says on the tin.
abbreviation	Approximately 3 character KEGG abbreviation.
species	If you do not have the abbreviation, this will try to find it.
savefile	Currently unused I think, but eventually should make a savefile of the results.

elsayed-lab/hpgltools documentation built on May 9, 2024, 5:02 a.m.